CODEWITHSUNDEEP
rlabelape-phylo
user3311610
user3311610

Reputation: 1

subtrees() in R ape package - how are internal nodes labeled in subtree?

I'm working with the ape package in R. I want a list of every possible subtree from a phylogenetic tree. I then want to iterate through the list of subtrees and get the root of every subtree. My question is, is the first internal node listed for each subtree the root of that subtree?

An example might illustrates my question better. I created a random tree with 12 tips, then extract the subtrees. I've copied the output for subtree 1. R then lists a couple of things including Node labels: 13, 14, ... for each subtree. Is the first node listed in Node labels (in this case node 13) always the root of the subtree?

phy = rtree(12)

st = subtrees(phy)

>st[[1]]

> st

[[1]]

Phylogenetic tree with 12 tips and 11 internal nodes.

Tip labels:
    t12, t2, t10, t1, t9, t4, ...

Node labels:
    13, 14, 15, 16, 17, 18, ...

Rooted; includes branch lengths.

Upvotes: 0

Views: 1660

Answers (1)

Christoph Glur
Christoph Glur

Reputation: 1244

That seems to be the case. To verify, you can visualize the tree by converting it to a data.tree structure:

library(data.tree)
tr <- as.Node(phy)
print(tr)

This will show as:

                        levelName
1  13                            
2   ¦--t7                        
3   °--14                        
4       ¦--15                    
5       ¦   ¦--t5                
6       ¦   °--t6                
7       °--16                    
8           ¦--17                
9           ¦   ¦--18            
10          ¦   ¦   ¦--19        
11          ¦   ¦   ¦   ¦--20    
12          ¦   ¦   ¦   ¦   ¦--t2
13          ¦   ¦   ¦   ¦   °--t9
14          ¦   ¦   ¦   °--t12   
15          ¦   ¦   °--t4        
16          ¦   °--21            
17          ¦       ¦--22        
18          ¦       ¦   ¦--t3    
19          ¦       ¦   °--t1    
20          ¦       °--23        
21          ¦           ¦--t10   
22          ¦           °--t11   
23          °--t8

Upvotes: 1

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